The causes and consequences of genetic interactions (epistasis)
The same mutation can have different effects in different individuals. One important reason
for this is that the outcome of a mutation can depend on the genetic context in which it …
for this is that the outcome of a mutation can depend on the genetic context in which it …
The evolution, evolvability and engineering of gene regulatory DNA
Mutations in non-coding regulatory DNA sequences can alter gene expression, organismal
phenotype and fitness,–. Constructing complete fitness landscapes, in which DNA …
phenotype and fitness,–. Constructing complete fitness landscapes, in which DNA …
The power of multiplexed functional analysis of genetic variants
New technologies have recently enabled saturation mutagenesis and functional analysis of
nearly all possible variants of regulatory elements or proteins of interest in single …
nearly all possible variants of regulatory elements or proteins of interest in single …
MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect
Multiplex assays of variant effect (MAVEs), such as deep mutational scans and massively
parallel reporter assays, test thousands of sequence variants in a single experiment. Despite …
parallel reporter assays, test thousands of sequence variants in a single experiment. Despite …
Deep learning of the regulatory grammar of yeast 5′ untranslated regions from 500,000 random sequences
Our ability to predict protein expression from DNA sequence alone remains poor, reflecting
our limited understanding of cis-regulatory grammar and hampering the design of …
our limited understanding of cis-regulatory grammar and hampering the design of …
Development of a comprehensive genotype-to-fitness map of adaptation-driving mutations in yeast
Adaptive evolution plays a large role in generating the phenotypic diversity observed in
nature, yet current methods are impractical for characterizing the molecular basis and fitness …
nature, yet current methods are impractical for characterizing the molecular basis and fitness …
A statistical framework for analyzing deep mutational scanning data
Deep mutational scanning is a widely used method for multiplex measurement of functional
consequences of protein variants. We developed a new deep mutational scanning statistical …
consequences of protein variants. We developed a new deep mutational scanning statistical …
ACIDES: on-line monitoring of forward genetic screens for protein engineering
Forward genetic screens of mutated variants are a versatile strategy for protein engineering
and investigation, which has been successfully applied to various studies like directed …
and investigation, which has been successfully applied to various studies like directed …
High-throughput identification of adaptive mutations in experimentally evolved yeast populations
High-throughput sequencing has enabled genetic screens that can rapidly identify mutations
that occur during experimental evolution. The presence of a mutation in an evolved lineage …
that occur during experimental evolution. The presence of a mutation in an evolved lineage …
A fitness trade-off explains the early fate of yeast aneuploids with chromosome gains
S Pompei… - Proceedings of the …, 2023 - National Acad Sciences
The early development of aneuploidy from an accidental chromosome missegregation
shows contrasting effects. On the one hand, it is associated with significant cellular stress …
shows contrasting effects. On the one hand, it is associated with significant cellular stress …